SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q5H8B9 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MAGDSLSLPGMSLQLLVTLTCLLLTCALRERVPLSENVSHCELYLPPWGA    50
  51  LNGGSHQNPGILIANSGFQVPQGRSVWLNPLRDLVIRVQRGDQCKVTVLD   100
 101  FPRLQGALSPHQFPCDFGAQQVKYTHFGSPSSTRTRIQLQVRYDAGNSTL   150
 151  VLPFTLQVNVVFPKLQLVARNRPLKVFKVLGCSHAIDRRVLNFASRSRCR   200
 201  LTVLPHPGGPLPKYGLLVDTAGNPLSRGHLADCEAFIQAGVRYQHTTTPS   250
 251  SPSRDYVPMLVELLGPESQGTRSVEVLAQEYFQIQVRIQKRARSTAPIPS   300
 301  LAALMIVEVEQSLLTALTPDVLAAEDSESDPDDLVFNILNVPEAPPGHHG   350
 351  GQGYVVNTDDPLGLPVSFFTQKELRELKIAYRPPTGSSEGDHVFQLKLQV   400
 401  VDEDGDTSEPFAFMVVVKSMNVLAPIASYRGGLVVFEGQARPLSDALSFQ   450
 451  VSDKDNSKEIKIVAVRGLQHGQLVVHGAPAGCKNFTLADLSAGRVVYQHD   500
 501  GSDSYSDNIILKMEGEHHRVDFLFPITIVPVDDAAPVLTANMGLSVTEGQ   550
 551  VVQISPFVLCATDIDSEDSAILFVLEDEHLEGKEEETHEDLAPGSYSSSQ   600
 601  HPGNMLLRQAEPPSSLLYSDWHYVEKEGLYETVVTEWLQRDIMEGRLFFS   650
 651  HPGPHSPSPVAHLAFHVQDDQDPPNLSNQHFFTISIQPADTSQPQLSPET   700
 701  TLEMTVQGYQLTPFQQKYLQYTDQNSDEQNLWYTLLTRPTDADSNHQVQA   750
 751  GEIVLTDSPGRPIVHFTQTQVNHQKIAYRPPQRNLGIVPRVVQFTYKVED   800
 801  TAGNSVSGTFTVFLQPLNNQPPKVINRGFAVLEGDSFILGRGELNVSDPD   850
 851  TNDDQIFFILVWGPQHGHLQYFKKYMVPGESFMLADVINGSISYQNSRDQ   900
 901  TDSDVIYLEVSDGVHHIPITVQVSVQPTVADRSPGISITGTPVLATSLTV   950
 951  LENAASEITMDVTHGRKNTNDLMLSFIVEDKPKLGMILVNGWPAEQVTQE  1000
1001  DLLGGAVSYVHTSGEIGFQRVHDTFSFILSKDAYHRAMRDNILERVLVEV  1050
1051  TVLPVDNMAPKVLVRKPFIVYEGGKNLLTPQHVNIEDVDTSKDEILCTLT  1100
1101  VQPSSGYLENLAPAPGSEVSRAGNPISAFFVKDVRVGCINYVQSIHKGIE  1150
1151  PGADQFTFYCSDGINFSPKVLLPLTILPTNDEQPQLFTREFVVLEGMSRV  1200
1201  IDTSLVNGVDADFPSDKHFRLTVFPQHGQITQQLATGSKPIHSFTLQEIQ  1250
1251  EPSSIAYEHDDSESTEDSFEVWLSDGRHTTHTTVPIAVILVDDEVPQLTI  1300
1301  NDGLEIETGHSEIITNHILKAIDLDSDNKSLSFVLHSEPQQGLLQRLRKP  1350
1351  GGDAKHNLTVGMNFTQDEIDRGLIHYIHTGQGEAVDLKFDVTDGVNTLRD  1400
1401  RYFYITIDNSNSAVPEIVSKRVTLTEGNRMTLTTELLNTSDIHSPGEQLL  1450
1451  YSITRAPSTGHLESSDQPGEPMASFTQLQLARNKISYVHISNDKIKLDHF  1500
1501  ELRVTGGHHSESRIFRIFVTEQDNKKPTLTIQALALQRGDNIVVTPSQLT  1550
1551  VEDEDTPADFILFTITQIPIHGRILYNGSRPVTTFTKKDLTKSLIYCHDG  1600
1601  SETSKDSFSFTVTDGIHTGFYVFPDTSLETHVPQTVWIQISPFDDRLPQM  1650
1651  GINRGATALKLLHTGHLGFLITNEYLQATHQGVPHRLLTYKVTRGPEHGY  1700
1701  IVNAGLGNENTHMFTQADIDEMRVYYILNKGRGRATRDTFYFSVETRGGK  1750
1751  QLRNQPFHLNWAWISLEKEYYIVDEDSPFFEVTLRRGYLGGTSVVSIGTK  1800
1801  GDTAEENKDFKGKAPMLVQFSPGQSTATWRVGLIPDTKYETSETFQIILS  1850
1851  EPGAAALEFPEMATVEIVDPEDESTVYIPEAEYQLAEAVGEFLVPVRRSG  1900
1901  DTSQELTVICSTRPGSATGTIPSVQLSLSDYVSRPEDNTSMLHFEKDESE  1950
1951  KTCQVLIINDSLYEEEESFSIALSLPTGGQLGAKFPTARVTILADREDEP  2000
2001  ALHFECSEYHAEESAGYVEVAVWRRGTGLSQASSVIVRSRGTEEQAAEAG  2050
2051  TDYIGVRQHLHFSPGVSVQRLRVTILDDLPQPAFEGPEMFELLLQMPTGA  2100
2101  VIGEPNKTTVTINDSVTNCEECV                             2123

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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